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Signatures of natural selection in morphological quantitative traits in Argentinean populations of Senegalia gilliesii (Fabaceae)

Abstract

In order to elucidate the role of evolutionary forces in shaping the variation of quantitative traits in Senegalia gilliesii we evaluate seven phenotypic traits in three Argentinean populations, two of them sharing environmental and vegetation type conditions, and a third one ecologically differentiated from the former. The phenotypic traits were compared with molecular markers. Here, we search for signatures of selection by means of the comparison PST-FST . We assessed if the averages of the seven phenotypic traits were different among populations by means of ANOVA and we performed discriminant analysis of principal components (DAPC) for both morphological and molecular data. The ANOVA showed significant results only for two traits. For all foliar traits and two spine traits, the PST-FST comparison suggested the occurrence of stabilizing selection. The DAPC obtained from AFLP data showed three well defined groups of populations; when the same analysis was conducted with morphological data the scatterplot showed high overlapping among individuals and could not separate the populations. Overall, our findings suggest a prominent role of stabilizing selection in all foliar traits and stipular spine length. These results could be extrapolated to other tropical and subtropical acacias. Further studies are needed to analyse the mechanisms underlying genetic differentiation in natural populations of S. gilliesii, find its relationship with eco-geographical variables.

Key words
Senegalia gilliesii; AFLP; conservation and reforestation programmes; natural selection; phenotypic traits

INTRODUCTION

Biological populations of plant and animal species do not constitute uniform units but are usually subdivided, represented by many partially isolated subpopulations. The extent of both genetically and phenotypic differentiation among these sub-units over time depends on the relative contribution of interacting evolutionary processes (natural selection, genetic drift, migration and mutation) (Wright 1931WRIGHT S. 1931. Evolution in Mendelian populations. Genetics 16: 97-159., Holsinger & Weir 2009HOLSINGER KE & WEIR BS. 2009. Genetics in geographically structured populations: Defining, estimating and interpreting F(ST). Nat Rev Gen 10: 639-649.). Unveiling the causes and consequences of this differentiation may represent a significant contribution to the theoretical evolutionary biology and ecology fields as well as to applied realms (for example, forestry and conservation biology). One key question in conservation biology and domestication of profitable resources is determining to what degree population differentiation is caused by selective versus neutral processes (Leinonen et al. 2013LEINONEN T, MCCAIRNS RJ, O’HARA RB & MERILÄ J. 2013. QST - FST comparisons: evolutionary and ecological insights from genomic heterogeneity. Nature Reviews Genetics 14: 179-190.).

Between-population differentiation in neutral alleles, quantified by FST , shows the level of expected differentiation across populations caused by stochastic processes (genetic drift, gene exchange) (Wright 1943WRIGHT S. 1943. Isolation by distance. Genetics 28(2): 114-138.). QST is a quantitative genetic analogue of FST that measures the amount of genetic variance among populations relative to the total genetic variance for each trait (Merilä & Crnokrak 2001MERILÄ J & CRNOKRAK P. 2001. Comparison of genetic differentiation at marker loci and quantitative traits. J Evol Biol 14: 892-903., Whitlock 2008WHITLOCK MC. 2008. Evolutionary inference from QST. Mol Ecol 17: 1885-1896., Leinonen et al. 2013LEINONEN T, MCCAIRNS RJ, O’HARA RB & MERILÄ J. 2013. QST - FST comparisons: evolutionary and ecological insights from genomic heterogeneity. Nature Reviews Genetics 14: 179-190.). In wild populations, the phenotypic differentiation between them is approximated by the surrogate of QST , PST (Leinonen et al. 2006LEINONEN T, CANO JM, MÄKINEN H & MERILÄ J. 2006. Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks. J Evol Biol 19: 1803-1812., 2008, Saether et al. 2007SAETHER SA, FISKE P, KALAS JA, KURESOO A, LUIGUJOE L & PIERTNEY SB. 2007. Inferring local adaptation from QST-FST comparisons: neutral genetic and quantitative trait variation in European populations of great snipe. J Evol Biol 20: 1563-1576., Wojcieszek & Simmons 2012WOJCIESZEK JM & SIMMONS LW. 2012. Evidence for stabilizing selection and slow divergent evolution of male genitalia in a millipede (Antichiropus variabilis). Evolution 66: 1138-1153.). Quantification of PST is based on phenotypic measures of a trait in the wild in several individuals across a number of populations (Brommer 2011BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168., Pujol et al. 2008PUJOL B, WILSON AJ, ROSS RIC & PANNELL JR. 2008. Are Q(st) − F(st) comparisons for natural populations meaningful? Mol Ecol 17: 4782-4785., Ojeda et al. 2016OJEDA F, VAN DER NIET T, MALA MC, MIDGLEY J & SEGARRA-MORAGUES JG. 2016. Strong signature of selection in seeder populations but not in reprouters of the fynbos heath Erica coccinea (Ericaceae). Bot J Linn Soc 181: 115-126., Antoniazza et al. 2010ANTONIAZZA S, BURRI R, FUMAGALLI L, GOUDET J & ROULIN A. 2010. Local adaptation maintains clinal variation in melanin-based coloration of European barn owls (Tyto alba). Evolution 64: 1944-1954., Brommer et al. 2014BROMMER JE, HANSKI IK, KEKKONEN J & VAISANEN RA. 2014. Size differentiation in Finish house sparrows follows Bergmann´s rule with evidence of local adaptation. J Evol Biol 27: 737-747., Pometti et al. 2019POMETTI CAROLINA L, BESSEGA CECILIA F, CIALDELLA ANA M, EWENS M, SAIDMAN BEATRIZ O & VILARDI JUAN C. 2019. Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae). Bot J Linn Soc 191(1): 128-141. doi.org/10.1093/botlinnean/boz023.). The precise estimation of QST requires the foundation of provenance trails in order to correct for environmental factors, however in wild populations, the phenotypic differentiation, quantified by the PST may be used, with care, as a proxy to QST (Leinonen et al. 2008LEINONEN T, O’HARA RB, CANO JM & MERILÄ J. 2008. Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis. J Evol Biol 21: 1-17.). The evolutionary inferences, taking care of the pitfalls, are quite similar to those for QST . In the cases in which QST=FST the differentiation could be explained by genetic drift alone. If QST > FST the he differentiation can be attributed to directional selection. If QST < FST the occurrence of stabilising selection can be assumed.

Using PST as an approximation of QST involves bias due to nonadditive genetic variances or environmental factors and genotype-environment interactions (Pujol et al. 2008PUJOL B, WILSON AJ, ROSS RIC & PANNELL JR. 2008. Are Q(st) − F(st) comparisons for natural populations meaningful? Mol Ecol 17: 4782-4785.). Although it is thus not generally recommended to simplify QST by its phenotypic analogue PST , rearing individuals from different populations in a common environment may not be feasible (especially when working with long-living wild species) (Brommer 2011BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168.).

Morphological variation within plant species that occupy different habitats could be due to genetic differentiation among populations or to environmental effects (Yucedag & Gailing 2013YUCEDAG C & GAILING O. 2013. Morphological and genetic variation within and among four Quercus petraea and Q. robur natural populations. Turkish J Botany 37: 619-629.). Therefore, measurement, description and analysis of morphological variation are fundamental steps to answer questions of biological adaptability (Ge & Hong 1995GE S & HONG DY. 1995. Biosystematic studies on Adenophora potaninii Korsh. complex (Campanulaceae) III. Genetic variation andtaxonomic value of morphological characters. Acta Phytotaxonomica Sinica 33: 433-443.). Genetic variation underlying phenotypic traits and phenotypic plasticity are particularly important when the long-term stability of forest ecosystems is increasingly threatened by environmental stress and mismanagement. Yucedag & Gailing (2013)YUCEDAG C & GAILING O. 2013. Morphological and genetic variation within and among four Quercus petraea and Q. robur natural populations. Turkish J Botany 37: 619-629. studied morphological traits relative to cones and seeds in seven populations of Juniperus excelsa. They found differences for all traits and observed in several analyses that northern populations were more similar than southern ones, in spite of the absence of a correlation between morphological and geographical distances between populations. Then, this could be explained by different environmental conditions in northern and southern populations (Yucedag & Gailing 2013YUCEDAG C & GAILING O. 2013. Morphological and genetic variation within and among four Quercus petraea and Q. robur natural populations. Turkish J Botany 37: 619-629.). The case of Acacia karroo is quite similar, Mboumba & Ward (2008)MBOUMBA GB & WARD D. 2008. Phenotypic plasticity and local adaptation in two extreme populations of Acacia karroo. African Journal of Range and Forage Science 25(3): 121-130. studied two populations: one from the semi-desert Karoo in central South Africa and other from the eastern coast of South Africa, in a subtropical forest. They analysed several morphological traits like number of spines, spines length, stem diameter, etc. Their results showed that the most plastic traits were above- and below-ground biomass and spine length. Arid trees showed to have longer spines and greater stem diameter than forest trees. As the water level increased, stem diameter and above-ground biomass increased. Finally, local adaptation was observed for stem diameter and spine number (Mboumba & Ward 2008MBOUMBA GB & WARD D. 2008. Phenotypic plasticity and local adaptation in two extreme populations of Acacia karroo. African Journal of Range and Forage Science 25(3): 121-130.). Thus, the genetic characterization of natural forest resources is an essential step for a better understanding of genetic resources for the implementation of in-situ and ex-situ conservation activities (Turna et al. 2001TURNA I, UÇLER AO & YAHYAOÐLU Z. 2001. Genetic analyses of isoenzyme variations in cilicican fir (Abies cilicica Carr). Punjab Univ Res Bull 51: 99-107.). In this context, the characterization of local genetic resources is often based on the knowledge of variation in morphological characters (Delgado et al. 2001DELGADO JV, BARBA C, CAMACHO ME, SERENO FTPS, MARTINEZ A & VEGA-PLA JL. 2001. Caracterización de los animales domésticos en España. Anim Genet Res Inf 29: 7-18.). The previous examples of Juniperus excelsa and Acacia karroo reveal the importance of assessing the relation between morphological and ecological variation contributing to design the correct management strategy for forest species.

Because selection occurs on the whole organism and not on single traits independently (Lande & Arnold 1983LANDE R & ARNOLD SJ. 1983. The measurement of selection on correlated characters. Evolution 37: 1210-1226.), a complete characterization of adaptive variation in polygenic traits is required. A multivariate approach provides an alternative to evolutionary predictions and allows studying adaptation on several traits simultaneously (Chapuis et al. 2008CHAPUIS E, MARTIN G & GOUDET J. 2008. Effects of selection and drift on G-matrix evolution in a heterogeneous environment: a multivariate QST – FST test with the freshwater snail Galba truncatula. Genetics 180: 2151-2161., Martin et al. 2008MARTIN G, CHAPUIS E & GOUDET J. 2008. Multivariate QST-FST comparisons: a neutrality test for the evolution of the G matrix in structured populations. Genetics 180: 2135-2149.). This approach involves a multivariate neutrality test, which addresses more complex questions about specific phenotypic effects of different evolutionary process. The idea is to compare the among-population (D) and within-population (G) covariance matrices and to test the neutral pattern of D=2FST/(1−FST) G (e.g. Bertram et al. (2011)BERTRAM SM, FITZSIMMONS LP, MCAULEY EM, RUNDLE D & GORELICK R. 2011. Phenotypic covariance structure and its divergence for acoustic mate attraction signals among four cricket species. Ecol & Evol: 181-195. compare both matrices in crickets looking for evidences of selection; Costa e Silva et al. (2020)COSTA E SILVA J, POTTS BM & HARRISON PA. 2020. Population Divergence along a Genetic Line of Least Resistance in the Tree Species Eucalyptus globulus. Genes 11: 1-24. compare D and G matrices in Eucalyptus also tracking for signals of selection from a multivariate phenotype) . For the multivariate quantitative phenotype, the equivalent to the genetic variance is the within population genetic covariance matrix G, whereas the multivariate equivalent to the total among population phenotypic variance is represented by the phenotypic covariance matrix (D). G provides a powerful tool to move beyond retrospective analysis and to address more complex questions about phenotypic effects of different evolutionary process. Furthermore, G can identify evolutionary constraints and differences among populations in their potential to evolve and specifically predict the direction and rate of phenotypic divergence (adaptive or neutral) (McGuigan 2006MCGUIGAN K. 2006. Studying phenotypic evolution using multivariate quantitative genetics. Mol Ecol 15: 883-896.).

The genus Senegalia that belongs to the Fabaceae family, Caesalpinodeae subfamily (Azani et al. 2017AZANI N ET AL. 2017. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny: The Legume Phylogeny Working Group (LPWG). Taxon 66: 44-77.) has 12 species represented in Argentina (Rico-Arce 2007RICO-ARCE ML. 2007. American species of Acacia (Leguminosae: Mimosoideae). Comisión Nacional para el conocimiento y Uso de la Biodiversidad (CONABIO).). Senegalia gilliesii (Steud.) Seigler & Ebinger (2006)SEIGLER DS & EBINGER JE. 2006. Mimosacea Senegalia gilliesii. Phytologia 88(1): 52 (Acacia gilliesii Steud.; Acacia furcatispina Burkart) is distributed in South America, in Argentina, Bolivia and Paraguay, where it is commonly known as “garabato blanco”, “garabato macho”, “mochuelo”, “teatin”, “brea” or “tinticaco”, among others (Rico-Arce 2007RICO-ARCE ML. 2007. American species of Acacia (Leguminosae: Mimosoideae). Comisión Nacional para el conocimiento y Uso de la Biodiversidad (CONABIO).). The particular form of its spines, makes unmistakable its identification in the field. For comparisons with other species formerly comprised in a unique genus called Acacia, we would have referred to Acacia s. l.

The Acacia s. l. species generally, have the ability of being nitrogen fixers, they provide wood for fuel, medicinal extracts, tannins, gums, wood, fibres, shadow and food for wild and domestic animals (Pometti et al. 2012POMETTI CL, BESSEGA CF, VILARDI JC & SAIDMAN BO. 2012. Landscape genetic structure of natural populations of Acacia caven in Argentina. Tree Genet Genom 8(4): 911-924.). Although this is not a threatened species, some previous works recommend S. gilliesii, among other species of the genus, for reforestation programmes; moreover, its wood presents characteristics considered desirable for the forest exploitation (Bravo et al. 2006BRAVO S, GIMÉNEZ A & MOGLIA J. 2006. Caracterización anatómica del leño y evolución del crecimiento en ejemplares de Acacia aroma y Senegalia gilliesii en la Región Chaqueña, Argentina. Bosque 27: 146-154. https://dx.doi.org/10.4067/S0717-92002006000200009.). The natural regeneration of S. gilliesii is by means of seeds and its most important dispersion agent is the domestic livestock (bovine, ovine and equine. The seed germination is accelerated due to the process of scarification received in the herbivorous intestine (Abedini et al. 2000ABEDINI W, BOERI P, MARINUCCI L, RUSCITTI M & SCELZO L. 2000. Biotécnicas aplicadas a especies forestales nativas. Invest Agr Sist Recur For Vol 9: 31-43.). Studies on this species from the genetic point of view although very important for conservation and rational use are still very scarce.

Up to now, only one American species of Acacia s.l. (A. aroma Gillies ex Hook. & Arn. = Vachellia aroma Seigler and Ebinger) was studied in order to detect signs of natural selection by the PST-FST comparison (Pometti et al. 2019POMETTI CAROLINA L, BESSEGA CECILIA F, CIALDELLA ANA M, EWENS M, SAIDMAN BEATRIZ O & VILARDI JUAN C. 2019. Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae). Bot J Linn Soc 191(1): 128-141. doi.org/10.1093/botlinnean/boz023.). As pointed out by Pometti et al. (2019)POMETTI CAROLINA L, BESSEGA CECILIA F, CIALDELLA ANA M, EWENS M, SAIDMAN BEATRIZ O & VILARDI JUAN C. 2019. Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae). Bot J Linn Soc 191(1): 128-141. doi.org/10.1093/botlinnean/boz023. in the case A. aroma, the length of stipular spines and leaf size and shape are among the main quantitative traits of taxonomical importance for the genus and used in silvicultural management programmes (Mahmood et al. 2005MAHMOOD S, AHMED A, HUSSAIN A & ATHAR M. 2005. Spatial pattern of variation in populations of Acacia nilotica in semi-arid environment. Int J Environ Sci Tech 2(3): 193-199.). The remarkable variation observed for these traits in natural populations suggests the possibility of a genetic basis which might be subjected to selection programmes. The feasibility of such programmes depends greatly on the knowledge of the distribution and possible adaptive effect of these traits. In order to elucidate the role of evolutionary forces in shaping the variation of quantitative traits in S. gilliesii, we first studied the relationships of genetic and phenotypic variation by means of the PST-FST comparison, analysing seven phenotypic traits and AFLP markers; second, we assessed if the averages of the seven phenotypic traits were significantly different among populations by means of non-paramentric ANOVA and MANOVA; third, in order to study adaptation on several traits simultaneously, we compared the among-population (D) and within-population (G) covariance matrices and evaluated if the coefficient of proportionality between such matrices (ρ) is equal to the expectation under neutrality; and finally we performed discriminant analysis of principal components (DAPC) for both morphological and molecular data sets and compared the results obtained in order to recognize if the phenotypic traits discriminate the three populations with the same power as the AFLP data.

MATERIALS AND METHODS

In this work, two sample sites of Senegalia gilliesii belonging to two different eco-regions were studied in Argentina. Cerro de la Gloria (CG: -32.885; -68.892) (Mendoza province) belongs to the Monte eco-region and Pasaje Pozo Zuni (PP: -27.965933; -63.9242) (Santiago del Estero province) is in the Chaco eco-region. In each locality 20 adult trees were found and sampled. Previous structure analysis by means of AFLP markers showed the occurrence of three genetic populations (CG1, CG2 and PP) (Cerdeira et al. 2019CERDEIRA EN, SAIDMAN BO & POMETTI CL. 2019. Evidencias de estructura poblacional y estructura genética espacial a escala fina en poblaciones argentinas de Senegalia gilliesii (Fabaceae). Bol Soc Argent Bot 54: 79-91.). In the present work, we reanalysed the genotypic data matrix obtained previously (Cerdeira et al. 2019CERDEIRA EN, SAIDMAN BO & POMETTI CL. 2019. Evidencias de estructura poblacional y estructura genética espacial a escala fina en poblaciones argentinas de Senegalia gilliesii (Fabaceae). Bol Soc Argent Bot 54: 79-91.), based on this result.

Vouchers of representative individuals of each population were collected and one of them was deposited at the herbarium SI, Instituto de Botánica Darwinion, San Isidro, Buenos Aires, Argentina.

Data scoring and AFLP analysis

Each AFLP band was considered for presence (scored as 1) or absence (scored as 0). Non-hierarchical Wright’s (1978) FST , its signficance (based on G-test) as well as its 95% confidence intervals (based on 5000 bootstraps) were estimated with the package hierfstat (Goudet 2005GOUDET J. 2005. HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5: 184-186.) of the R software 4.0.2 (R Core Team 2020). This analysis was conducted in order to compare FST with the PST coefficient as described below.

Discriminant Analysis of Principal Components (DAPC)

DAPC was applied to AFLP data matrix using the adegenet package (Jombart 2008JOMBART T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405.) (function dapc, Jombart et al. 2010JOMBART T, DEVILLARD S & BALLOUX F. 2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11: 94.) for the software R (R Development Core Team 2020R DEVELOPMENT CORE TEAM. 2020. R: a language and environment for statistical computing. R Foundation for Statistical Computing: Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org.
http://www.R-project.org...
). This analysis was performed with prior information on individual populations found in Cerdeira et al. (2019)CERDEIRA EN, SAIDMAN BO & POMETTI CL. 2019. Evidencias de estructura poblacional y estructura genética espacial a escala fina en poblaciones argentinas de Senegalia gilliesii (Fabaceae). Bol Soc Argent Bot 54: 79-91..

Phenotypic analysis

We measured seven morphological traits on the 40 individuals sampled (10 for CG1, 10 for CG2 and 20 for PP). The morphological traits were measured on two replicates of the herbarium material and the average of these measurements was considered. The measurements were performed with a millimetric ruler and, when necessary, were made under a magnifying glass. All the measurements were made by the same person (CP). The morphological traits were chosen based on their use in silvicultural activities and as forage. Besides, leaf and spines are important from the taxonomic point of view. Fruit morphology was not taken into account since it is considered as a uniform character for the entire genus Senegalia. The following morphological characters were measured: rachis length (cm) (RAL), pairs of leaflets on the apical pinna (PLA), pairs of leaflets on the basal pinna (PLB), left stipular spine length (cm) (SSLl), right stipular spine length (cm) (SSLr), minimum base of stipular spine length (cm) (BSL min), maximum base of stipular spine length (cm) (BSL max) (Fig. 1). The original data matrix is available upon request from the corresponding author.

Figure 1
Senegalia gilliesii specimen exemplifying the studied morphological traits. a- Branch with flowers, leafs and stipular spines; b- amplification of the stipular spines. RAL: rachis length (cm), PLA: pairs of leaflets on the apical pinna, PLB: pairs of leaflets on the basal pinna, SSLl: left stipular spine length (cm), SSLr: right stipular spine length (cm), BSL min: minimum base of stipular spine length (cm), BSL max: maximum base of stipular spine length (cm). Image modified from the “Flora de Jujuy, de la Flora del Conosur, Catalogo de plantas Vasculares” Instituto de Botánica Darwinion, darwin.edu.ar.

The differences among populations for each trait were evaluated by a nonparametric Kruskal & Wallis (1952)KRUSKAL WH & WALLIS WA. 1952. Use of ranks in one criterion variance analysis. J Am Stat Assoc 47: 586-621. ANOVA test. We choose this test because it is a distribution-free method that does not require any assumption about trait distribution. In the cases when the test was significant, Dunn’s post-hoc multiple comparisons were conducted for each trait in order to identify which population (s) was different from each other. These analyses were carried out with the software Statistica 5.5 (StatSoft Inc. 2000STATSOFT INC. 2000. STATISTICA for Windows 5.5 (Computer Program Manual). StatSoft, Inc., 2300 East 14th Street, Tulsa O.K.).

Moreover, MANOVA test was performed in order to cover more than one dependent variable that cannot be combined in a simple way. This test, tries to identify the degree of association of a multivariate response with the independent variable. This analysis was also performed with the software Statistica 5.5 (StatSoft Inc. 2000STATSOFT INC. 2000. STATISTICA for Windows 5.5 (Computer Program Manual). StatSoft, Inc., 2300 East 14th Street, Tulsa O.K.).

The variance in phenotypic values within and between populations was assessed via PST coefficient (Brommer 2011BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168., Pujol et al. 2008PUJOL B, WILSON AJ, ROSS RIC & PANNELL JR. 2008. Are Q(st) − F(st) comparisons for natural populations meaningful? Mol Ecol 17: 4782-4785.). The surrogate of QST is defined by the expression:

P S T = σ B 2 σ B 2 + 2 ( σ W 2 ) (1)

where σB 2 is the phenotypic variance between groups and σW 2 is the phenotypic variance within groups.

The variance components for this statistic were estimated from the following linear random model:

y i j k = μ + p i + l j + e i j k (2)

where yijk is the phenotypic measure of the repeat k in individual j from population i, μ is the general mean, p represent the random effect of population, l is the random individual effect, and e is the residual error. These components were estimated with the function lmer of the package lme4 (Bates et al. 2015BATES D, MAECHLER M, BOLKER B & WALKER S. 2015. Fitting Linear Mixed-Effects Models Using lme4. J Statistical Softw 67(1): 1-48. doi:10.18637/jss.v067.i01.) of R software 3.4.3 (R Core Team 2020). The inferences of directional selection were limited to traits for which the confidence intervals of PST do not overlap with those of FST and PST FST . Stabilizing selection inference, in time, was limited to traits for which PSTFST with no overlapping confidence intervals (Brommer 2011BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168.).

The complete formula to calculate PST is (Brommer 2011BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168.):

P S T = ( c / h 2 ) σ B 2 ( c / h 2 ) σ B 2 + 2 ( σ W 2 ) (3)

where the ratio c/h 2 is the proportion of additive variance across populations relative to the within-population heritability. When compared with the neutral expectation based on the differentiation of AFLP bands in the same populations (e.g., PST-FST ), an approximation of the extent to which selection drives the differentiation was obtained by estimating PST under the assumption of c/h 2=1. More details about this comparison and its inferences could be read in Brommer et al. (2014)BROMMER JE, HANSKI IK, KEKKONEN J & VAISANEN RA. 2014. Size differentiation in Finish house sparrows follows Bergmann´s rule with evidence of local adaptation. J Evol Biol 27: 737-747. and Pometti et al. (2019)POMETTI CAROLINA L, BESSEGA CECILIA F, CIALDELLA ANA M, EWENS M, SAIDMAN BEATRIZ O & VILARDI JUAN C. 2019. Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae). Bot J Linn Soc 191(1): 128-141. doi.org/10.1093/botlinnean/boz023..

In this work, the covariance matrices D and G were calculated and was evaluated if the coefficient of proportionality between such matrices (ρ) was equal to the expectation under neutrality, that is:

ρ = D / G = 2 F S T / 1 F S T

The comparison between expected and observed ρ was made by means of a t test: t= (ρexp – ρobs)/Se

where Se is the standard error of the ρobs estimated.

The covariance matrices D and G were obtained using the package MCMCglmm (Hadfield 2009HADFIELD JD. 2009. MCMC methods for Multi-response Generalised Linear Mixed Models: The MCMCglmm R Package.) of R. The running conditions were: n° iterations=130000, thinning=100, burnin=30000, retaining the 1000 final iterations.

Discriminant Analysis of Principal Components (DAPC) was applied to phenotypic data matrix using the adegenet package (Jombart 2008JOMBART T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405.) (function dapc, Jombart et al. 2010JOMBART T, DEVILLARD S & BALLOUX F. 2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11: 94.) for the software R (R Development Core Team 2020R DEVELOPMENT CORE TEAM. 2020. R: a language and environment for statistical computing. R Foundation for Statistical Computing: Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org.
http://www.R-project.org...
). As in the case of AFLP, this analysis was performed with prior information on individual populations.

RESULTS

The AFLP analysis previously reported (Cerdeira et al. 2019CERDEIRA EN, SAIDMAN BO & POMETTI CL. 2019. Evidencias de estructura poblacional y estructura genética espacial a escala fina en poblaciones argentinas de Senegalia gilliesii (Fabaceae). Bol Soc Argent Bot 54: 79-91.) showed a total of 121 discernible bands in the 40 individuals belonging to the three populations studied (CG1, CG2 and PP), ranging from 90 to 400bp with three combinations of selective primers.

The estimate of the non-hierarchical FST was 0.27 (CI95%= 0.22-0.32), indicating highly significant genetic differences between the populations.

Analysis of variance

The comparison of morphological differences among populations (Table I) showed significant differences only for BSL max and BSL min (Fig. 2). Dunn’s contrasts showed significant differences between PP and CG2 for BSL max, and that PP differs from CG1 and CG2 for BSL min.

Figure 2
Box-plot comparisons of phenotypic traits measured among three populations of S. gilliesii. A) RAL, B) PLB, C) PLA, D) SSLl, E) SSLr, F) BSL min, G) BSL max. Statistical significance at 0.05 level for non- parametric ANOVA. Full squares represent the mean of the trait for each population; empty squares represent the mean ± SD; and vertical lines represent the mean ± SEM.
Table I
Basic statistics of the three populations of S. gilliesii studied. Mean, SD: standard deviation of each trait, N= 40. K-W ANOVA: Non parametric Kruskal-Wallis ANOVA, H: values of test statistic, P: statistical significance. RAL: rachis length, PLA: pairs of leaflets on the apical pinna, PLB: pairs of leaflets on the basal pinna, SSLl: left stipular spine length, SSLr: right stipular spine length, (BSL min) minimum base of stipular spine length, (BSL max) maximum base of stipular spine length. **P≤0.01

According to the multivariate analysis of variance (MANOVA) differences among populations were highly significant (P= 0.003).

Phenotypic variation

The phenotypic differentiation (PST ) ranged from 3.73 x 10-10 for right stipular spine length (SSLr) to 0.15 for maximum basal spine length (BSL max). These estimates were compared with those of the molecular differentiation between populations assessed from the 121AFLP loci. In all cases PST were lower than FST , although for BSL max and BSL min, the 95% CI overlapped (Fig. 3), indicating that the Ho of neutrality cannot be rejected. For the remaining traits (RAL, PLB, PLA, SSLl and SSLr) the differences between PST and FST were significant (95% CI did not overlap, Fig. 3). The critical c/h2 values for SSLr and PLB are 0.24 and 0.73, respectively (Table II), meaning that the upper 95% confidence interval of PST would not overlap the lower 95% confidence interval of FST .

Figure 3
Pairwise phenotypic differentiation (PST) values (±95% CI) for the seven traits in the three populations of S. gilliesii. Vertical dashed lines denote the upper and lower 95% confidence intervals of pairwise FST obtained from AFLP data. FST value estimated with the total (121) AFLP data set.
Table II
PST values and c/h2 for the seven traits analysed.

The comparison between D and G matrices did not reject the hypothesis of proportionality (ρ= 1.011, P= 4x 10-9). This observed value for ρ was compared with the expected one calculated as 2FST/(1-FST)= 0.74. The difference between the observed and expected ρ, was significant (t= 1.92, P= 0.03, df=48).

Discriminant Analysis of Principal Components (DAPC)

DAPC was first made for the AFLP data set. The clusters were defined a priori, according to the genetic population. In this case, 2 axes were retained for DAPC, explaining the 83.38% and the 16.62% respectively. The scatterplot showed three well defined groups of populations (Fig. 4a). When the same analysis was conducted with morphological data, also 2 axes were retained for the DAPC, explaining the 90.7% and the 9.3% respectively, but the scatterplot showed high overlapping among individuals and could not separate the populations by neither the two axes (Fig. 4b).

Figure 4
Plot of Discriminant Analysis of Principal Components (DAPC)1 and 2 of S. gilliesii populations. a- from AFLP data; b- from morphological data.

DISCUSSION

Little is known about how selective forces are acting in tropical and subtropical Acacia species in general. The first genetic study in S. gilliesii, showed a high percentage of polymorphic loci, high mean heterozygosity estimated with AFLP markers, showed also that most part of variation resides within populations and SGS was detected at short and middle distances (Cerdeira et al. 2019CERDEIRA EN, SAIDMAN BO & POMETTI CL. 2019. Evidencias de estructura poblacional y estructura genética espacial a escala fina en poblaciones argentinas de Senegalia gilliesii (Fabaceae). Bol Soc Argent Bot 54: 79-91.). All these results are in accordance with those obtained for other American and African species of the genera Senegalia and Vachellia. In the present work we study for the first time a species of the genus Senegalia using the PST-FST comparison to track for signals of natural selection in S. gilliesii. We assessed seven quantitative traits and the existence of differences between populations and analysed the results obtained aiming to determinate the evolutionary forces modulating differentiation.

When applying the PST- FST comparison it is important to not confound the effects in additive genetic variance of the environment (Merilä Crnokrak 2001MERILÄ J & CRNOKRAK P. 2001. Comparison of genetic differentiation at marker loci and quantitative traits. J Evol Biol 14: 892-903., Pujol et al. 2008PUJOL B, WILSON AJ, ROSS RIC & PANNELL JR. 2008. Are Q(st) − F(st) comparisons for natural populations meaningful? Mol Ecol 17: 4782-4785.). To patch this issue, the approach of Brommer (2011)BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168. incorporates the environment effects between populations by evaluating the effect of between-population additive genetic variance (c) to within-population additive variance relative to total variance (h 2). Therefore is paramount to see the point when the ratio c/h 2 is smaller and the PST exceeds FST . In that point, the support for local adaptation for a particular trait is stronger (Brommer 2011BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168.). In this sense, the evaluation of the c/h 2 ratio allows a more rigorous test of natural selection making more robust the estimate of PST. However, in the case of the CG vs. PP, the differences between populations could be attributed at least partially to phenotypic plasticity as a response to variation. In order to confirm the trends observed in this paper a larger sampling involving a higher number of populations and provenance tests under uniform conditions would be needed. However, plasticity in phenotypic responses would probably produce an overestimation rather than an underestimation of genetic variation quantified by PST what suggest that our conclusion of stabilising selection is well supported.

In this work, five of the seven traits measured showed evidence of stabilizing selection. The critical c/h 2 values obtained here for the PSTs, could be considered moderately high, supporting the robustness of the results (Brommer 2011BROMMER JE. 2011. Whither P(st)? The approximation of Q(st) by P(st) in evolutionary and conservation biology. J Evol Biol 24: 1160-1168.). Three of them are foliar traits (RAL, PLB and PLA) and the other two refer to the length of the stipular spines. The same traits measured in seven populations of A. aroma (=V. aroma) gave similar results, all showing signs of stabilizing selection (Pometti et al. 2019POMETTI CAROLINA L, BESSEGA CECILIA F, CIALDELLA ANA M, EWENS M, SAIDMAN BEATRIZ O & VILARDI JUAN C. 2019. Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae). Bot J Linn Soc 191(1): 128-141. doi.org/10.1093/botlinnean/boz023.) evidencing a similar trend for these traits in American Acacia s. l. species. Other American woody Caesalpinoideae species showed similar results, for example in Prosopis flexuosa, four leaf traits evidenced stabilizing selection (Darquier et al. 2013DARQUIER MR, BESSEGA CF, CONY M, VILARDI JC & SAIDMAN BO. 2013. Evidence of heterogeneous selection on quantitative traits of Prosopis flexuosa (Leguminosae) from multivariate Q ST –F ST test. Tree Genetics & Genomes 9: 307-320. https://doi.org/10.1007/s11295-012-0556-x.); the same trend was observed in P. alba for three foliar traits and spine length (Bessega et al. 2015BESSEGA C, POMETTI C, EWENS M, SAIDMAN BO & VILARDI JC. 2015. Evidences of local adaptation in quantitative traits in Prosopis alba (Leguminosae). Genetica 143: 31-44.). Finally, in P. chilensis stabilizing selection was described for spine length based on FST-QST test and DJOST and δGREGORIUS alternative coefficients of differentiation (Chequer Charan et al. 2020CHEQUER CHARAN D, POMETTI C, CONY M, VILARDI JC, SAIDMAN BO & BESSEGA CF. 2020. Genetic variance distribution of SSR markers and economically important quantitative traits in a progeny trial of Prosopis chilensis (Leguminosae): implications for the ‘Algarrobo’ management programme. Forestry: An International Journal of Forest Research, cpaa026, https://doi.org/10.1093/forestry/cpaa026.
https://doi.org/10.1093/forestry/cpaa026...
). In summary, Argentinean related woody legume species showed the same trend to uniform selection in at least some foliar traits.

When plants grow or are adapted to a resource-rich environment, they generally invest more energy in growth, but when the environment have poor resources they invest more in defence, like spine length (Coley et al. 1985COLEY PD, BRYANT JP & CHAPIN FS III. 1985. Resource availability hypothesis and plant antiherbivore defence. Science 230: 895-899.). In this work, there was no evidence of differences in stipular spines length among populations, suggesting there is no difference in resources among environments. Similar results for spine length were found by Mboumba Ward (2008)MBOUMBA GB & WARD D. 2008. Phenotypic plasticity and local adaptation in two extreme populations of Acacia karroo. African Journal of Range and Forage Science 25(3): 121-130., assessing two populations of Acacia karroo of contrasting environments.

According to some authors (Martin et al. 2008MARTIN G, CHAPUIS E & GOUDET J. 2008. Multivariate QST-FST comparisons: a neutrality test for the evolution of the G matrix in structured populations. Genetics 180: 2135-2149., Chapuis et al. 2008CHAPUIS E, MARTIN G & GOUDET J. 2008. Effects of selection and drift on G-matrix evolution in a heterogeneous environment: a multivariate QST – FST test with the freshwater snail Galba truncatula. Genetics 180: 2151-2161.) a multivariate analysis provides a more accurate picture of the impact of selection versus drift on the system as a whole. In this work, G and D matrices are proportional. Taken as whole the results suggest that different regimes may be acting on different traits: stabilizing selection and neutrality (Fig. 3). Moreover, the MANOVA was significant due to the influence of two traits: BSL max and BSLmin, however these traits resulted selectively neutral in accordance to the PST value. In future projects more populations could be included if possible in order to recover to the maximum the existing morphological variation in this species for these traits and be able to solve this question.

In this study, the multivariate DAPC analysis showed a better discrimination of the populations in clear clusters when analysing the molecular data matrix rather than the morphological one. This result showed a consistency when those results obtained with Canonical Discriminant Analysis in the species under the name of Acacia aroma (Pometti et al. 2019POMETTI CAROLINA L, BESSEGA CECILIA F, CIALDELLA ANA M, EWENS M, SAIDMAN BEATRIZ O & VILARDI JUAN C. 2019. Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae). Bot J Linn Soc 191(1): 128-141. doi.org/10.1093/botlinnean/boz023.). This is not the first time that molecular markers discriminate better groups that morphology; in previous work in other Acacias this was also observed (Pometti et al. 2010POMETTI CL, VILARDI JC, CIALDELLA AM & SAIDMAN BO. 2010. Genetic diversity among the six varieties of Acacia caven (Leguminosae, Mimosoideae) evaluated at molecular and phenotypic levels. Plant Systemat Evol 284: 187-199. DOI 10.1007/s00606-009-0244-y., Pometti et al. 2019POMETTI CAROLINA L, BESSEGA CECILIA F, CIALDELLA ANA M, EWENS M, SAIDMAN BEATRIZ O & VILARDI JUAN C. 2019. Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae). Bot J Linn Soc 191(1): 128-141. doi.org/10.1093/botlinnean/boz023.). These results were explained based on the neutrality of the molecular markers (Strauss et al. 1992STRAUSS SH, BOUSQUET J, HIPKINS VD & HONG YP. 1992. Biochemical and molecular genetic markers in biosystematic studies of forest trees. New Forests 6: 125-158.) and the large coverage along all the genome (Stammers et al. 1995STAMMERS M, HARRIS J, EVANS G M, HAYWARD MD & FORSTER JW. 1995. Use of random PCR (RAPD) technology to analyse phylogenetic relationships in the Lolium/Festuca complex. Heredity 74: 19-27.). So, both data should be complemented, that obtained by molecular markers and the morphological characterization (Artyukova et al. 2000ARTYUKOVA EV, KOZYRENKO MM, REUNOVA GD, MUZAROK TI & ZHURAVLEV YU N. 2000. RAPD analysis of genome variability of planted ginseng, Panax ginseng. Mol Biol 34: 339-344., Li et al. 2002LI X, RALPHS MH, GARDNER DR & WANG RRC. 2002. Genetic variation within and among 22 accessions of three tall larkspur species (Delphinium spp.) based on RAPD markers. Biochem Syst Ecol 30: 91-102., 2008LI F, GAN S, WENG Q, ZHAO X, HUANG S, LI M, CHEN S, WANG Q & SHI F. 2008. RAPD and morphological diversity among four populations of the tropical tree species Paramichelia baillonii (Pierre) Hu in China. Forest Ecol Manag 255: 1793-1801.). For this reason, in all these cases, molecular markers discriminate populations better than phenotypic traits which may be affected by selection.

Overall, our findings suggest a prominent role of stabilizing selection in all foliar traits and stipular spine length although there was no evidence of significant differentiation among populations for these characters. These results could be extrapolated to other tropical and subtropical acacias belonging to the genus Senegalia in particular, although also are consistent with the findings for A. aroma (= V. aroma). Further study is needed to analyse the mechanisms underlying genetic differentiation in natural populations of S. gilliesii, and try to find its relationship with eco-geographical variables.

ACKNOWLEDGMENTS

The authors of the present paper want to thanks to Dr. Soledad Albanese from IADIZA, CONICET, Mendoza and Ing. Mauricio Ewens from Estación Experimental Fernandez, Santiago del Estero for the collection of part of the material of study. Also, we want to thank to Dr. Fernando Zuloaga from IBODA, CONICET for kindly let us use an image of the Flora de Jujuy. Finally, we want to thank for the financial support to the Agencia Nacional de Promoción Científica y Tecnológica (PICT-2016-0388 to C. L. P) and CONICET (PIP 11220130100191 to C. L. P.) and UNIVERSIDAD DE BUENOS AIRES (UBACYT 20020190200106BA).

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Publication Dates

  • Publication in this collection
    22 Oct 2021
  • Date of issue
    2021

History

  • Received
    19 Oct 2020
  • Accepted
    21 July 2021
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